[Bioc-devel] makeTxDbPackage bugs in Bioconductor 3.5

[Keith Hughitt]

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.

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.

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]]