If I am not mistaken the same problem is on the support site and I provided some commentary at https://support.bioconductor.org/p/117265/#117312
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://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
