[BioC] [ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9

[Dan Tenenbaum]

On Mon, Jun 4, 2012 at 11:18 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> (cc'ing list, for posterity)
>
> On 06/02/2012 01:22 PM, Martin Morgan wrote:
>>
>> On 06/02/2012 01:08 PM, sheng zhao wrote:
>>>
>>> Hi Martin,
>>>
>>> My answer is yes. Please see following:
>>>
>>>
>>> mac$ R --vanilla
>>>
>>> R version 2.15.0 (2012-03-30)
>>> Copyright (C) 2012 The R Foundation for Statistical Computing
>>> ISBN 3-900051-07-0
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>> > library(GO.db)
>>> Loading required package: AnnotationDbi
>>>
>>> Loading required package: BiocGenerics
>>>
>>> Attaching package: 'BiocGenerics'
>>>
>>> The following object(s) are masked from 'package:stats':
>>>
>>> xtabs
>>>
>>> The following object(s) are masked from 'package:base':
>>>
>>> Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
>>> colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
>>> order, paste, pmax, pmax.int <http://pmax.int>, pmin, pmin.int
>>> <http://pmin.int>, rbind, rep.int <http://rep.int>,
>>> rownames, sapply, setdiff, table, tapply, union, unique
>>>
>>> Loading required package: Biobase
>>> Welcome to Bioconductor
>>>
>>> Vignettes contain introductory material; view with
>>> 'browseVignettes()'. To cite Bioconductor, see
>>> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>>>
>>> Loading required package: DBI
>>> Error : .onLoad failed in loadNamespace() for 'GO.db', details:
>>> call: ls(envir, all.names = TRUE)
>>> error: 7 arguments passed to .Internal(identical) which requires 6
>>> Error: package/namespace load failed for 'GO.db'
>>>
>>

I experienced the same problem, but fixed it by following Prof.
Ripley's advice and updating to R-patched (which you can get at
http://r.research.att.com/).

Thanks,
Dan



>> I am looking at Prof. Ripley's post here
>>
>>
>> http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal-identical-which-requires-6-td4548460.html
>>
>>
>> and the time stamp on your version of R (March 30). I do not really have
>> a good suggestion; perhaps (a) traceback() after the error; (b)
>> installing GO.db from source (biocLite("GO.db", type="source")). And since
>>
>> trace(loadNamespace, tracer=quote(print(package)))
>> library(GO.db)
>>
>> ends with
>>
>> Loading required package: DBI
>> Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry
>> [1] "DBI"
>> Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry
>> [1] "RSQLite"
>>
>> for me these two packages also are candidates for suspicion.
>>
>> Martin
>>
>>
>>
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor