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

[Steve Lianoglou]

Hi,

On Fri, Jun 1, 2012 at 11:09 AM, sheng zhao <harryzs1981 at gmail.com> wrote:
> Dear all,
>
> I updated ChIPpeakAnno to 2.5.9 by:
>
> useDevel(TRUE)
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("ChIPpeakAnno")
>
>
>
> After that, I got the following wrong Error information when starting
> ChIPpeakAnno:
>
> 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
>
>
> Any suggestion? Thanks .
>
> ps: Working with ChIPpeakAnno 2.4.0 is fine.

I suspect you'll need to upgrade the rest of your packages to their
devel versions if you want to use the devel version of ChIPpeakAnno
(using the devel version works for me).

In light of the yearly R release cycle now, the bioc folks have
outlined a strategy you might want to follow if you think you want to
hop between release and devel versions of packages here:

http://bioconductor.org/developers/useDevel/

HTH,
-steve

>
> Regards,
> Sheng
>
>> sessionInfo()
> 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_1.15.11
>  [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
>
> 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
>
>        [[alternative HTML version deleted]]
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact