Hi Herve, Thanks for your response and for the new version. Evetything works well now. Cheers, Giorgos 2013/11/5 Hervé Pagès <hpages@fhcrc.org> > Hi George, > > Thanks for the report. This should be fixed in IRanges 1.20.5 (release) > and 1.21.8 (devel), which should become available tru biocLite() in the > next 24 hours or so. > > Cheers, > H. > > > On 11/04/2013 03:59 AM, George Baskozos wrote: > >> Hi, >> I have found a recently introduced bug. The bug is present in >> GenomicRanges >> 1.14.3 but not in GenomicRanges 1.12.5. >> >> Example to illustrate the bug: >> >> >> example(GRanges) >>> mycov = coverage(longGR) >>> rle.i = slice(mycov, lower=3) >>> gr = as (rle.i, "GRanges") >>> >> Error in normalizeSingleBracketSubscript(i, x) : invalid subscript type >> >>> >>> sessionInfo() >>> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] BiocInstaller_1.12.0 GenomicRanges_1.14.3 XVector_0.2.0 >> [4] IRanges_1.20.4 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] stats4_3.0.2 tools_3.0.2 >> >> >> Using previous versions the example is working properly. Just to >> illustrate >> it: >> >> example(GRanges) >>> mycov = coverage(longGR) >>> rle.i = slice(mycov, lower=3) >>> gr = as (rle.i, "GRanges") >>> gr >>> >> GRanges with 20 ranges and 2 metadata columns: >> seqnames ranges strand | score view >> <rle> <iranges> <rle> | <integer> <integer> >> [1] chr1 [2, 2] * | 3 1 >> [2] chr1 [3, 4] * | 4 1 >> [3] chr1 [5, 6] * | 5 1 >> [4] chr1 [7, 7] * | 4 1 >> [5] chr1 [8, 10] * | 3 1 >> ... ... ... ... ... ... ... >> [16] chr3 [ 9, 9] * | 6 1 >> [17] chr3 [ 10, 10] * | 8 1 >> [18] chr3 [ 11, 11] * | 4 1 >> [19] chr3 [ 12, 12] * | 3 1 >> [20] chr3 [110, 117] * | 3 2 >> --- >> seqlengths: >> chr1 chr2 chr3 >> NA NA NA >> >>> >>> sessionInfo() >>> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] GenomicRanges_1.12.5 IRanges_1.18.4 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] stats4_3.0.2 tools_3.0.2 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@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@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]