Hi Hubert, Martin, This should be fixed in GenomicRanges 1.6.7 (release) and 1.7.24 (devel). Those new versions should become available thru biocLite() in the next 24-36 hours. Please let me know if you still have problems with this. Thanks, H. On 01/20/2012 07:17 AM, Martin Morgan wrote: > On 01/20/2012 05:14 AM, Hubert Rehrauer wrote: >> Hi >> >> There seems to be an overvflow problem if the GappedAlignments object >> holds many reads: > > Yes that looks like a bug; it will take some time to be fixed. Thanks. > Martin > >> >> With foo being a gapped alignments having 17836148 reads I get: >>> bar = narrow( foo[1:10000000], di[1:10000000]) ## fine >>> bar = narrow( foo[10000000:17836148], di[10000000:17836148]) ## fine >>> bar = narrow( foo, di) >>> Error during wrapup: in 'cigar' element 11380048: CIGAR is empty after >>> narrowing >>> Warning messages: >>> 1: In successiveIRanges(cigarToWidth(cigar)) : >>> Integer overflow in 'cumsum'; use 'cumsum(as.numeric(.))' >>> 2: In start(x) + width(x) : NAs produced by integer overflow >>> 3: In start(x) + width(x) : NAs produced by integer overflow >>> 4: In start(x) + width(x) : NAs produced by integer overflow >> can you help??? >> >> hubert >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- 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: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319