[Bioc-devel] select(Homo.sapiens,...) failing

[Obenchain, Valerie]

Hi Vince,

You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing
check because of the biomart problems so you'll have to get it from svn.
Let me know if you still have problems after updating.

Val


On 05/02/2016 11:53 AM, Vincent Carey wrote:
> biocValid() says all is well ...
>
>> select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL")
> *Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : *
>
> *  object '.testSelectArgs' not found*
>
>> sessionInfo()
> R version 3.3.0 beta (2016-04-01 r70412)
>
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> Running under: OS X 10.10.5 (Yosemite)
>
>
> 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  stats4    stats     graphics  grDevices utils     datasets
>
> [8] methods   base
>
>
> other attached packages:
>
>  [1] Homo.sapiens_1.3.1
>
>  [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
>
>  [3] org.Hs.eg.db_3.3.0
>
>  [4] GO.db_3.3.0
>
>  [5] OrganismDbi_1.13.8
>
>  [6] GenomicFeatures_1.23.31
>
>  [7] GenomicRanges_1.23.27
>
>  [8] GenomeInfoDb_1.7.6
>
>  [9] AnnotationDbi_1.33.15
>
> [10] IRanges_2.5.46
>
>
> [11] S4Vectors_0.9.52
>
> [12] Biobase_2.31.3
>
> [13] BiocGenerics_0.17.5
>
> [14] BiocInstaller_1.21.6
>
>
> loaded via a namespace (and not attached):
>
>  [1] graph_1.49.1                Rcpp_0.12.4.5
>
>  [3] XVector_0.11.8              zlibbioc_1.17.1
>
>  [5] GenomicAlignments_1.7.21    BiocParallel_1.5.22
>
>  [7] tools_3.3.0                 SummarizedExperiment_1.1.27
>
>  [9] DBI_0.4                     RBGL_1.47.0
>
> [11] rtracklayer_1.31.11         bitops_1.0-6
>
> [13] RCurl_1.95-4.8              biomaRt_2.27.2
>
> [15] RSQLite_1.0.0               Biostrings_2.39.14
>
> [17] Rsamtools_1.23.11           XML_3.98-1.4
>
> 	[[alternative HTML version deleted]]
>
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>



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