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.

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 Mu??oz [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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >