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

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

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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

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