[BioC] curious IRanges error when sort()ing a GRanges

[Hervé Pagès]

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

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