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

[Martin Morgan]

On 06/02/2012 01:00 PM, sheng zhao wrote:
> Hi Martin,
>
> thank you for your help.
>
> Follow your guide :
> ------
>   source('http://bioconductor.org/biocLite.R')
>   biocLite(character())
> ------
>
> I updated all old packages.
> I also checked the version of GO.db
>
>  > packageDescription("GO.db")$Version
> [1] "2.7.1"
>
>
> But I am very sorry to say that I still face this problem.:

Does, in a new R --vanilla session, simply trying to load GO.db cause 
the problem,

   library(GO.db)

?

>
>
>  > library(ChIPpeakAnno)
> Loading required package: gplots
> Loading required package: gtools
> Loading required package: gdata
> gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
>
> gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
>
> Attaching package: 'gdata'
>
> The following object(s) are masked from 'package:stats':
>
>      nobs
>
> The following object(s) are masked from 'package:utils':
>
>      object.size
>
> Loading required package: caTools
> Loading required package: bitops
> Loading required package: grid
> Loading required package: KernSmooth
> KernSmooth 2.23 loaded
> Copyright M. P. Wand 1997-2009
>
> Attaching package: 'gplots'
>
> The following object(s) are masked from 'package:stats':
>
>      lowess
>
> Loading required package: BiocGenerics
>
> Attaching package: 'BiocGenerics'
>
> The following object(s) are masked from 'package:gdata':
>
>      combine
>
> 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: biomaRt
> Loading required package: multtest
> 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")'.
>
>
> Attaching package: 'multtest'
>
> The following object(s) are masked from 'package:gplots':
>
>      wapply
>
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:gplots':
>
>      space
>
> The following object(s) are masked from 'package:caTools':
>
>      runmean
>
> The following object(s) are masked from 'package:gdata':
>
>      trim
>
> Loading required package: Biostrings
> Loading required package: BSgenome
> Loading required package: GenomicRanges
> Loading required package: BSgenome.Ecoli.NCBI.20080805
> Loading required package: GO.db
> Loading required package: AnnotationDbi
>
> Attaching package: 'AnnotationDbi'
>
> The following object(s) are masked from 'package:BSgenome':
>
>      species
>
> 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 'GO.db' could not be loaded
>
>
>
>  > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] RSQLite_0.11.1                      DBI_0.2-5
>   [3] AnnotationDbi_1.19.9
>   BSgenome.Ecoli.NCBI.20080805_1.3.17
>   [5] BSgenome_1.25.1                     GenomicRanges_1.9.21
>   [7] Biostrings_2.25.4                   IRanges_1.15.12
>   [9] multtest_2.13.0                     Biobase_2.17.5
> [11] biomaRt_2.13.1                      BiocGenerics_0.3.0
> [13] gplots_2.10.1                       KernSmooth_2.23-7
> [15] caTools_1.13                        bitops_1.0-4.1
> [17] gdata_2.8.2                         gtools_2.6.2
> [19] BiocInstaller_1.5.10
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-18      RCurl_1.91-1     XML_3.9-4        splines_2.15.0
> [5] stats4_2.15.0    survival_2.36-14 tools_2.15.0
>  > source('http://bioconductor.org/biocLite.R')
>  >  biocLite(character())
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.5.10.
>
>


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