> -----Original Message----- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Kasper Daniel Hansen > Sent: Saturday, October 10, 2015 11:04 PM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] error in stable AnnotationHub > > Using Bioconductor 3.1 and the following code > > library(AnnotationHub) > ah <- AnnotationHub() > ah[["AH28868"]] > > I get an error like
It seems like the record is expecting additional columns in the bed file, but it contains only ranges and score; spot checking on the hotspot.broad.bed files suggests that they all have this format. Will address, but in the mean time a workaround is rtracklayer::import(cache(ah["AH28868"]), format="bed", genome="hg19") Martin > > retrieving 1 resources > > |========================================================= > =============| > 100% > Error in value[[3L]](cond) : > failed to load hub resource ‘E003-DNase.hotspot.broad.bed.gz’ of class > EpigenomeRoadmapFile; reason: length of 'chrom' greater than length > of 'ranges' > In addition: There were 50 or more warnings (use warnings() to see the first > 50) > > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
