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

[Martin Morgan]

(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 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
>
>
>
>


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