Thank you Herve! Then, I will pull the code from github to update my code, too.
Hopefully my package will also go through by 24th :) Best, Bora ________________________________________ From: Hervé Pagès [hpa...@fredhutch.org] Sent: Monday, October 23, 2017 6:17 AM To: Uyar, Bora; bioc-devel@r-project.org Subject: Re: [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.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: > 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.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://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= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
