[Bioc-devel] makeTxDbPackage bugs in Bioconductor 3.5

[Obenchain, Valerie]

Hi Keith,

On 02/08/2017 11:37 AM, Keith Hughitt wrote:
> Greetings,
>
> I came across a couple issues when working with the most recent version of
> GenomicFeatures (Bioconductor 3.5/Github).
>
> 1) The "Resource URL" metadata field is only set via some of the helper
> functions (e.g. makeTxDbFromBiomart), but not others. Since it is required
> by makeTxDbPackage, the function will fail if passed a txdb constructed
> using something like makeTxDbFromGFF:
>
> Error in makeTxDbPackage(txdb, version = settings$db_version, maintainer =
> settings$maintainer,  :   values for symbols SOURCEURL are not single
> strings
>
> Should be easy to fix by modifying the other makeTxDbFromXX functions to
> specify the Resource URL.

The only makeTxDb* function that does not have the ability to pass
metadata fields is makeTxDbFromGFF(). I think the 'dataSource' arg was
intended for this purpose (at least in part) but it's unfortunate it was
given a different name.

I've added a 'metadata' arg to makeTxDbFromGFF(). This is a data.frame
that can pass any number of metadata fields. I've included an example of
passing 'Resource URL' at the bottom of the man page.

>
> 2) The final expression in the function (saveDb(txdb, file=db_path)) fails
> sometimes because the output directory "PKG/inst/extdata" may not exist.
> Adding a call to `dir.create()` shortly before this function call fixes the
> issue.

Thanks. Now fixed.

Changes are in GenomicFeatures 1.27.8 which should be available via
biocLite() Saturday Feb 11 around noon PST.

Valerie

>
> Cheers,
> Keith
>
> ---
>
>> sessionInfo()
> R Under development (unstable) (2017-01-08 r71936)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Arch Linux
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] GenomicFeatures_1.27.6 AnnotationDbi_1.37.2   Biobase_2.35.0
>  [4] rtracklayer_1.35.5     GenomicRanges_1.27.22  GenomeInfoDb_1.11.8
>  [7] IRanges_2.9.18         S4Vectors_0.13.13      BiocGenerics_0.21.3
> [10] yaml_2.1.14            colorout_1.1-2
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.9                XVector_0.15.2
>  [3] zlibbioc_1.21.0            GenomicAlignments_1.11.9
>  [5] BiocParallel_1.9.5         lattice_0.20-34
>  [7] tools_3.4.0                SummarizedExperiment_1.5.4
>  [9] grid_3.4.0                 DBI_0.5-1
> [11] digest_0.6.12              Matrix_1.2-7.1
> [13] bitops_1.0-6               biomaRt_2.31.4
> [15] RCurl_1.95-4.8             memoise_1.0.0
> [17] RSQLite_1.1-2              compiler_3.4.0
> [19] Biostrings_2.43.4          Rsamtools_1.27.12
> [21] XML_3.98-1.5
>
> 	[[alternative HTML version deleted]]
>
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