Sweet, works great. Thanks Herve! R> packageVersion('IRanges') [1] ‘1.13.34’ R> head(sort(hg19.by.arm)) GRanges with 6 ranges and 0 elementMetadata cols: seqnames ranges strand <rle> <iranges> <rle> chr1p chr1 [ 1, 121535433] * chr1q chr1 [124535435, 249250621] * chr10p chr10 [ 1, 39254934] * chr10q chr10 [ 42254936, 135534747] * chr11p chr11 [ 1, 51644204] * chr11q chr11 [ 54644206, 135006516] * --- seqlengths: chr1 chr10 chr11 chr12 ... chr9 chrX chrY 249250621 135534747 135006516 133851895 ... 141213431 155270560 59373566 2012/3/26 Hervé Pagès <hpages@fhcrc.org> > Hi Tim, > > This regression was introduced in IRanges 1.13.33 and is fixed in > IRanges 1.13.34. > > Cheers, > H. > > > > On 03/26/2012 10:58 AM, Tim Triche, Jr. wrote: > >> R> sort(hg19.by.arm) >> Error in x[order(x, decreasing = decreasing)] : >> error in evaluating the argument 'i' in selecting a method for function >> '[': Error in .Call2("Integer_order4", a, b, c, d, decreasing, PACKAGE = >> "IRanges") : >> 'a', 'b', 'c' and 'd' must be integer vectors >> >> This only just started happening yesterday. On machines with older >> GenomicRanges/IRanges installs, it doesn't happen. Any ideas when/how the >> regression might have occurred? >> >> I tried debugging it but that didn't go anywhere useful. (sorry) I did >> load up a fresh session with only a GenomicRanges object (saved to disk) >> and it still crapped out with the above, though. >> >> R> sessionInfo() >> R Under development (unstable) (2012-03-07 r58622) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 >> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 >> LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] splines parallel grid stats graphics grDevices datasets >> utils methods >> [10] base >> >> other attached packages: >> [1] BSgenome.Hsapiens.UCSC.hg19_1.**3.17 BSgenome_1.23.4 >> [3] Biostrings_2.23.6 pint_1.7.03 >> [5] dmt_0.7.06 Matrix_1.0-5 >> [7] lattice_0.20-6 mvtnorm_0.9-9992 >> [9] idiogram_1.31.2 plotrix_3.3-9 >> [11] annotate_1.33.8 AnnotationDbi_1.17.27 >> [13] cRank_0.8 energy_1.4-0 >> [15] MASS_7.3-17 boot_1.3-4 >> [17] rtracklayer_1.15.8 WGCNA_1.19 >> [19] reshape_0.8.4 plyr_1.7.1 >> [21] cluster_1.14.2 Hmisc_3.9-2 >> [23] survival_2.36-12 flashClust_1.01-1 >> [25] dynamicTreeCut_1.21 impute_1.29.1 >> [27] zoo_1.7-7 genoset_1.4.21 >> [29] GenomicRanges_1.7.38 IRanges_1.13.33 >> [31] Gviz_0.99.9 data.table_1.7.10 >> [33] bigmemory_4.2.11 methylumi_2.1.17 >> [35] ggplot2_0.9.0 reshape2_1.2.1 >> [37] scales_0.2.0 Biobase_2.15.4 >> [39] BiocGenerics_0.1.14 RMySQL_0.9-3 >> [41] DBI_0.2-5 corpcor_1.6.2 >> [43] RCytoscape_1.5.25 XMLRPC_0.2-4 >> [45] graph_1.33.1 BiocInstaller_1.3.9 >> [47] devtools_0.6 gtools_2.6.2 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.11.2 bitops_1.0-4.1 colorspace_1.1-1 >> dichromat_1.2-4 >> [5] digest_0.5.2 DNAcopy_1.29.1 memoise_0.1 munsell_0.3 >> [9] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 >> Rsamtools_1.7.41 >> [13] RSQLite_0.11.1 stats4_2.16.0 stringr_0.6 tools_2.16.0 >> [17] XML_3.9-4 xtable_1.7-0 zlibbioc_1.1.1 >> >> > > -- > 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 > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]