[Bioc-devel] makeTxDbPackage bugs in Bioconductor 3.5
Valerie.Obenchain at roswellpark.org
Fri Feb 10 04:47:32 CET 2017
On 02/08/2017 11:37 AM, Keith Hughitt wrote:
> 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
> 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
Thanks. Now fixed.
Changes are in GenomicFeatures 1.27.8 which should be available via
biocLite() Saturday Feb 11 around noon PST.
> R Under development (unstable) (2017-01-08 r71936)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Arch Linux
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=en_US.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  parallel stats4 stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  GenomicFeatures_1.27.6 AnnotationDbi_1.37.2 Biobase_2.35.0
>  rtracklayer_1.35.5 GenomicRanges_1.27.22 GenomeInfoDb_1.11.8
>  IRanges_2.9.18 S4Vectors_0.13.13 BiocGenerics_0.21.3
>  yaml_2.1.14 colorout_1.1-2
> loaded via a namespace (and not attached):
>  Rcpp_0.12.9 XVector_0.15.2
>  zlibbioc_1.21.0 GenomicAlignments_1.11.9
>  BiocParallel_1.9.5 lattice_0.20-34
>  tools_3.4.0 SummarizedExperiment_1.5.4
>  grid_3.4.0 DBI_0.5-1
>  digest_0.6.12 Matrix_1.2-7.1
>  bitops_1.0-6 biomaRt_2.31.4
>  RCurl_1.95-4.8 memoise_1.0.0
>  RSQLite_1.1-2 compiler_3.4.0
>  Biostrings_2.43.4 Rsamtools_1.27.12
>  XML_3.98-1.5
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