Hi Bora,
I just fixed this in GenomicFeatures 1.29.15. The error on the build
report won't clear until Tuesday Oct 24 though.
Cheers,
H.
On 10/22/2017 02:59 PM, bora.u...@mdc-berlin.de wrote:
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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_GenomicFeatures_commit_22b2ea0a81bc064b8554400ce8f7e13e2c833d38&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=bz4mjLoa7FjycKUx_wCB7Ic1b2nOpTJt0J69fXSaasQ&e=).
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:
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email: bora.u...@mdc-berlin.de<mailto:bora.u...@mdc-berlin.de>
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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