Hi there, I answered this yesterday on the support site:
https://support.bioconductor.org/p/117265/#117346 Cheers, H. On 1/26/19 05:13, Vincent Carey wrote: > If I am not mistaken the same problem is on the support site and I provided > some > commentary at > https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_117265_-23117312&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XxwgvJX7-_q4u4p3uuJwItb8au40MB3h_gED2Ol9cXg&s=WKYBXF18xN-CQSEQtk0VghwXznKY3rcf94AR_IVcPfI&e= > > Let's keep the discussion there. The "problem" seems to be upstream at > UCSC. There > may be a design approach that avoids the risk of asynchrony between > separate resources > and community input can be useful on this. > > > On Fri, Jan 25, 2019 at 10:42 PM 陈施航 < > chen.shih...@genome.rcast.u-tokyo.ac.jp> wrote: > >> Hi GenomicFeatures support, >> >> I am Shihang Chen, a phD student at the University of Tokyo, using >> GenomicFeatures for ChIPSeeker. >> I run into a problem when I was using makeTxDbFromUCSC, and really need >> your help. >> >> After I run >> txdb=makeTxDbFromUCSC(genome="hg19",tablename="refGene") >> I got this error. >> Download the refGene table ... OK >> Download the hgFixed.refLink table ... OK >> Extract the 'transcripts' data frame ... OK >> Extract the 'splicings' data frame ... OK >> Download and preprocess the 'chrominfo' data frame ... OK >> Prepare the 'metadata' data frame ... OK >> *Make the TxDb object ... Error in .check_foreign_key(transcripts_tx_chrom, >> NA, "transcripts$tx_chrom", : * >> * all the values in 'transcripts$tx_chrom' must be present in >> 'chrominfo$chrom'* >> >> I consider the problem is that refGene version was upgraded last >> November,however, GenomicFeatures haven't done corresponding changes to the >> new refGene release. >> I attached my survey report in this email. >> If you have any clues why this is happening, please let me know. >> Your help is much appreciated. >> Thank you so much! >> >> Shihang Chen >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XxwgvJX7-_q4u4p3uuJwItb8au40MB3h_gED2Ol9cXg&s=ZJNp-sK9VzvuJnoEM7n9rOkPECujgzbZHRsunathFnk&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
