[Bioc-devel] Package failure due to GenomicFeatures update
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.Uyar at 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-R?ssle-Str. 10, 13125, Berlin, Germany Building 89, Room 1.08 web: https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinformatics.mdc-2Dberlin.de_team.html-23bora-2Duyar-2Dphd&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=9gkC_jhjUe4nWpERCOvchonLiz90IwwrayNY4zEsYSE&e= email: bora.uyar at mdc-berlin.de<mailto:bora.uyar at mdc-berlin.de> office tel: +49 30 9406 1802 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=goCJ-xKRJaiSn68lr8aP4w7yW1ZQMc9lFunuDYuSSIY&e=
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