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.u...@mdc-berlin.de<mailto:bora.u...@mdc-berlin.de> office tel: +49 30 9406 1802 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
