[Bioc-devel] Package failure due to GenomicFeatures update

Bora.Uyar at mdc-berlin.de Bora.Uyar at mdc-berlin.de
Sun Oct 22 23:59:39 CEST 2017


I am the maintainer of the RCAS package. Currently, my package build report shows errors related to the latest commit to GenomicFeatures package (See https://github.com/Bioconductor/GenomicFeatures/commit/22b2ea0a81bc064b8554400ce8f7e13e2c833d38). GenomicFeatures is showing errors because of the same reason.

This is an excerpt from the GenomicFeatures build report:
"# Creation time: 2017-10-22 00:29:43 -0400 (Sun, 22 Oct 2017)

# GenomicFeatures version at creation time: 1.29.14
# RSQLite version at creation time: 2.0
> ## Reverse operation:
> gr2 <- asGFF(txdb)
> ## Sanity check:
> stopifnot(identical(as.list(txdb), as.list(makeTxDbFromGRanges(gr2))))
Error in .get_cds_IDX(type, phase) :
  when 'gr' contains CDS features, it must have a "phase" metadata column
  and the phase must be 0, 1, or 2, for all the CDS features
Calls: stopifnot ... identical -> as.list -> makeTxDbFromGRanges -> .get_cds_IDX
Execution halted”

The build report for RCAS shows the same error. However, I cannot fix this problem because I can only install GenomicFeatures version 1.29.13, but the bioc-build system is using GenomicFeatures v1.29.14.

Do you know when this will be solved?



Dr. Bora Uyar

Bioinformatics Scientist
Scientific Bioinformatics Platform
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrueck Center (MDC) for Molecular Medicine

Robert-Rössle-Str. 10, 13125, Berlin, Germany
Building 89, Room 1.08

web: http://bioinformatics.mdc-berlin.de/team.html#bora-uyar-phd
email: bora.uyar at mdc-berlin.de<mailto:bora.uyar at mdc-berlin.de>
office tel: +49 30 9406 1802

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list