[BioC] org.Hs.eg.db package loading issues

[Dan Tenenbaum]

On Fri, Jul 26, 2013 at 8:41 AM, Guest [guest] <guest at bioconductor.org> wrote:
>
> Hi,
>
> When I run the R code on analysis of HuGene2.0ST array, it generated an error as follows:
>
>> source("/Users/jial2/Documents/projects/Project422/limmaAnalysis.R")
> Loading required package: org.Hs.eg.db
> Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
>   call: get(name, envir = asNamespace(pkg), inherits = FALSE)
>   error: object '.setDummyField' not found
> Error: package ‘org.Hs.eg.db’ could not be loaded
>
> Then I run the library individually, it still has the same error message.
>
>> library(org.Hs.eg.db)
> Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
>   call: get(name, envir = asNamespace(pkg), inherits = FALSE)
>   error: object '.setDummyField' not found
> Error: package or namespace load failed for ‘org.Hs.eg.db’
>
> Any suggestions would be highly appreciated.
>


This problem can be solved by updating to R 3.0.1.
Dan


> Thanks,
>
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] AnnotationDbi_1.22.6       limma_3.16.6               pd.hugene.2.0.st_3.8.0
>  [4] RSQLite_0.11.4             DBI_0.2-7                  oligo_1.24.1
>  [7] oligoClasses_1.22.0        affyPLM_1.36.0             preprocessCore_1.22.0
> [10] arrayQualityMetrics_3.16.0 affyQCReport_1.38.0        lattice_0.20-15
> [13] simpleaffy_2.36.1          gcrma_2.32.0               genefilter_1.42.0
> [16] affy_1.38.1                Biobase_2.20.1             BiocGenerics_0.6.0
> [19] BiocInstaller_1.10.2
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.32.3    affyio_1.28.0        annotate_1.38.0      beadarray_2.10.0
>  [5] BeadDataPackR_1.12.0 Biostrings_2.28.0    bit_1.1-10           Cairo_1.5-2
>  [9] cluster_1.14.4       codetools_0.2-8      colorspace_1.2-2     ff_2.2-11
> [13] foreach_1.4.1        GenomicRanges_1.12.4 grid_3.0.0           Hmisc_3.12-2
> [17] hwriter_1.3          IRanges_1.18.2       iterators_1.0.6      KernSmooth_2.23-10
> [21] latticeExtra_0.6-24  plyr_1.8             RColorBrewer_1.0-5   reshape2_1.2.2
> [25] rpart_4.1-1          setRNG_2011.11-2     splines_3.0.0        stats4_3.0.0
> [29] stringr_0.6.2        survival_2.37-4      SVGAnnotation_0.93-1 tools_3.0.0
> [33] vsn_3.28.0           XML_3.95-0.2         xtable_1.7-1         zlibbioc_1.6.0
>
> --
> 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