[BioC] 'version' is missing error when running makeTxDbPackageFromUCSC

[Dan Tenenbaum]

On Tue, Aug 27, 2013 at 3:18 PM, Michael Steeves <steeves at raingods.net> wrote:
> On OS X (10.8.4) with R 3.0.1, I'm getting an error when running the
> following three lines of code:
>
> library(GenomicRanges)
> library(GenomicFeatures)
> txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene')
>
> Download the refGene table ... OK
> Download the refLink table ... OK
> Extract the 'transcripts' data frame ... OK
> Extract the 'splicings' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Prepare the 'metadata' data frame ... OK
> Make the TranscriptDb object ... OK
> Error in list(PKGTITLE = paste("Annotation package for", dbType,
> "object(s)"),  :
>   'version' is missing


This means you have to supply a 'version' argument. See
?makeTxDbPackageFromUCSC

Dan



> In addition: There were 50 or more warnings (use warnings() to see the first
> 50)
>
> If I run this on RHEL5, the same code fails in the same place, though with a
> slightly different error message:
>
>> txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene')
> Download the refGene table ... OK
> Download the refLink table ... OK
> Extract the 'transcripts' data frame ... OK
> Extract the 'splicings' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Prepare the 'metadata' data frame ... OK
> Make the TranscriptDb object ... Error in .Call2("svn_time", PACKAGE =
> "IRanges") :
>   IRanges internal error in svn_time(): get_svn_time() failed
> In addition: There were 50 or more warnings (use warnings() to see the first
> 50)
>
> For OS X:
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin12.4.0 (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
> [8] base
>
> other attached packages:
> [1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6 Biobase_2.20.1
> [4] GenomicRanges_1.12.5   IRanges_1.18.1 BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] biomaRt_2.16.0     Biostrings_2.28.0 bitops_1.0-5       BSgenome_1.28.0
>  [5] DBI_0.2-7          RCurl_1.95-4.1 Rsamtools_1.12.3   RSQLite_0.11.4
>  [9] rtracklayer_1.20.3 stats4_3.0.1 tools_3.0.1        XML_3.98-1.1
> [13] zlibbioc_1.6.0
>
> For RHEL:
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
> [1] GenomicFeatures_1.12.2 AnnotationDbi_1.22.5   Biobase_2.20.0
> [4] GenomicRanges_1.12.4   IRanges_1.18.3 BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] BSgenome_1.28.0    Biostrings_2.28.0  DBI_0.2-7 RCurl_1.95-4.1
>  [5] RSQLite_0.11.4     Rsamtools_1.12.3   XML_3.96-1.1 biomaRt_2.16.0
>  [9] bitops_1.0-5       rtracklayer_1.20.2 stats4_3.0.1 tools_3.0.1
> [13] zlibbioc_1.6.0
>
> The warnings referenced don't look related, I don't think:
>
> 43: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],
> ... :
>   UCSC data anomaly in transcript NM_010707: the cds cumulative length is
> not a multiple of 3
>
>
> -Mike
> --
> Michael Steeves (steeves at raingods.net)
>
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