[BioC] PREDA command does not work

[Valerie Obenchain]

Hi Maria,

The errors tell you that the XML package is not installed and the 
annotate package could not be loaded because it depends on XML. PREDA 
cannot be loaded because it depends on annotate.

Are you using biocLite() to install packages? Have you tried,

     library(BiocInstaller)
     biocLite("XML")

If this does not fix the problem, please provide the output of 
sesssionInfo() and any error messages you see.

Valerie



On 06/26/2013 04:54 AM, Maria Arnedo Muñoz [guest] wrote:
>
> Hello!
>
> I am working with the PREDA package. I upload the package but it gives me this error  when it is uploading:
>
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>    there is no package called ‘XML’
> Error: package ‘annotate’ could not be loaded
>
> Then when I try to work with the command statisticsForPREDAfromEset or another specific PREDA command the following error appears:
>
> Error: could not find function "statisticsForPREDAfromEset"
>
> Any suggestion?? I don't know what could be happened!
>
> Thank you!
>
> Best regards
>
> Maria
>
>
>   -- output of sessionInfo():
>
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.4          DBI_0.2-7
>   [4] oligo_1.22.0            oligoClasses_1.20.0     affy_1.36.1
>   [7] AnnotationDbi_1.20.7    multtest_2.14.0         lokern_1.1-3
> [10] Biobase_2.18.0          BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.30.2     affyio_1.26.0         BiocInstaller_1.8.3
>   [4] Biostrings_2.26.3     bit_1.1-10            codetools_0.2-8
>   [7] ff_2.2-11             foreach_1.4.1         GenomicRanges_1.10.7
> [10] IRanges_1.16.6        iterators_1.0.6       MASS_7.3-23
> [13] parallel_2.15.3       preprocessCore_1.20.0 sfsmisc_1.0-23
> [16] splines_2.15.3        stats4_2.15.3         survival_2.37-4
> [19] xtable_1.7-1          zlibbioc_1.4.0
>>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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