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

[Vincent Carey]

Thanks Val that did the trick.

On Mon, May 2, 2016 at 4:40 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> 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]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
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