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

-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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