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

[Martin Morgan]

On 06/02/2012 12:25 AM, sheng zhao wrote:
> Hi Steve,
>
> thank you for your help.
>
> But I still face this problem even after I reinstalled R (version 2.15.0)
>   and reinstalled all packages I need to devel versions .
>
> With other packages I am using, for example: cummerbund 1.99.2, under devel
> version
> , everything is working fine.
>
> I tested also all thing on windows, everything is working under devel
> versions.
>
> Is it a bug for Mac 10.7.4 ?

Steve is right that the problem is likely to be an outdated package; it 
is NOT related to operating system.

Start a new R session, making sure that no '.Rhistory' or '.RData' are 
loaded (e.g., from the command line, R --vanilla) then issue the command

   source('http://bioconductor.org/biocLite.R')
   biocLite(character())

this should report any out-of-date packages; can you please post the 
result of this command?

Since the original error occurred with GO.db, perhaps you could also 
report the result of packageDescription("GO.db")$Version.

Can you simplify your session, e.g., cummbeRbund, fastcluster, reshape, 
and ggplot2 are not loaded by ChIPpeakAnno.

Martin

>
> Regards,
> Sheng
>
> 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] cummeRbund_1.99.2                   fastcluster_1.1.6
>
>   [3] reshape2_1.2.1                      ggplot2_0.9.1
>
>   [5] RSQLite_0.11.1                      DBI_0.2-5
>
>   [7] AnnotationDbi_1.19.9                BSgenome.Ecoli.NCBI.20080805_1.3.17
>
>   [9] BSgenome_1.25.1                     GenomicRanges_1.9.21
>
> [11] Biostrings_2.25.4                   IRanges_1.15.11
>
> [13] multtest_2.13.0                     Biobase_2.17.5
>
> [15] biomaRt_2.13.1                      BiocGenerics_0.3.0
>
> [17] gplots_2.10.1                       KernSmooth_2.23-7
>
> [19] caTools_1.13                        bitops_1.0-4.1
>
> [21] gdata_2.8.2                         gtools_2.6.2
>
> [23] BiocInstaller_1.5.10
>
>
> loaded via a namespace (and not attached):
>
>   [1] MASS_7.3-18        RColorBrewer_1.0-5 RCurl_1.91-1       XML_3.9-4
>
>
>   [5] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2       labeling_0.1
>
>
>   [9] memoise_0.1        munsell_0.3        plyr_1.7.1
> proto_0.3-9.2
>
> [13] scales_0.2.1       splines_2.15.0     stats4_2.15.0      stringr_0.6
>
>
> [17] survival_2.36-14   tools_2.15.0
>
> 	[[alternative HTML version deleted]]
>
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