[Bioc-devel] makeTxDbPackage bugs in Bioconductor 3.5

Keith Hughitt khughitt at umd.edu
Wed Feb 8 20:14:02 CET 2017


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.

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



> sessionInfo()
R Under development (unstable) (2017-01-08 r71936)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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

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