[Bioc-devel] Package failure due to GenomicFeatures update

[Bora.Uyar at mdc-berlin.de]

Hi,

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
# DBSCHEMAVERSION: 1.2
>
> ## 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?

Best,
Bora

_____________

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


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