Thanks. I knew about this but have been unable to fix it. It is some sort
of memory error. It happens in IRanges C code but the corruption could be
happening from read.chain(). There haven't been any consequential changes
to read.chain. Must just be showing up now. Haven't been able to find any
obvious errors in read.chain.

On Mon, Dec 5, 2011 at 2:52 PM, Leonardo Collado Torres
<lcollado@jhsph.edu>wrote:

> Hello BioC-list,
>
> I've been organizing some code for a local package, and was doing so in R
> 2.13.1. I just installed R 2.14.0 today and I found out that the liftOver
> function from the rtracklayer package no longer works. The example for that
> function is defined as:
>
> > example(liftOver)
>
> lftOvr> ## Not run:
> lftOvr> ##D chain <- import.chain("hg19ToHg18.over.chain")
> lftOvr> ##D library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> lftOvr> ##D tx_hg19 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
> lftOvr> ##D tx_hg18 <- liftOver(tx_hg19, chain)
> lftOvr> ## End(Not run)
> lftOvr>
> lftOvr>
> lftOvr>
> >
>
> So, I simply tried re-running the example. Note that I had the chain file
> from before on our local package bumphunter.
>
> > library(GenomicRanges); library(rtracklayer)
> Loading required package: IRanges
>
> Attaching package: ‘IRanges’
>
> The following object(s) are masked from ‘package:base’:
>
>    cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
>    pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
> Loading required package: RCurl
> Loading required package: bitops
> > chain <- import.chain(system.file("extdata", "hg19ToHg18.over.chain",
> package="bumphunter"))
> > chain
> Chain of length 25
> names(25): chr22 chr21 chr19 chr20 chr18 chrY ... chr6 chr5 chr4 chr3 chr2
> chr1
> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> Loading required package: GenomicFeatures
> Loading required package: AnnotationDbi
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'browseVignettes()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation("pkgname")'.
>
>
> Attaching package: ‘Biobase’
>
> The following object(s) are masked from ‘package:IRanges’:
>
>    updateObject
>
> > tx_hg19 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
> > tx_hg18 <- liftOver(tx_hg19, chain)
> Discarding unchained sequences: chr6_ssto_hap7, chr6_mcf_hap5,
> chr6_cox_hap2, chr6_mann_hap4, chr6_apd_hap1, chr6_qbl_hap6, chr6_dbb_hap3,
> chr17_ctg5_hap1, chr4_ctg9_hap1, chr1_gl000192_random, chrUn_gl000225,
> chr4_gl000194_random, chr4_gl000193_random, chr9_gl000200_random,
> chrUn_gl000222, chrUn_gl000212, chr7_gl000195_random, chrUn_gl000223,
> chrUn_gl000224, chrUn_gl000219, chr17_gl000205_random, chrUn_gl000215,
> chrUn_gl000216, chrUn_gl000217, chr9_gl000199_random, chrUn_gl000211,
> chrUn_gl000213, chrUn_gl000220, chrUn_gl000218, chr19_gl000209_random,
> chrUn_gl000221, chrUn_gl000214, chrUn_gl000228, chrUn_gl000227,
> chr1_gl000191_random, chr19_gl000208_random, chr9_gl000198_random,
> chr17_gl000204_random, chrUn_gl000233, chrUn_gl000237, chrUn_gl000230,
> chrUn_gl000242, chrUn_gl000243, chrUn_gl000241, chrUn_gl000236,
> chrUn_gl000240, chr17_gl000206_random, chrUn_gl000232, chrUn_gl000234,
> chr11_gl000202_random, chrUn_gl000238, chrUn_gl000244, chrUn_gl000248,
> chr8_gl000196_random, chrUn_gl000249, chrUn_gl000246,
> chr17_gl000203_random, chr8_gl000197_random, chrUn_gl000245,
> chrUn_gl000247, chr9_gl000201_random, chrUn_gl000235, chrUn_gl000239,
> chr21_gl000210_random, chrUn_gl000231, chrUn_gl000229, chrUn_gl000226,
> chr18_gl000207_random
> Error in unlist(mseqapply(liftOverSpace, rl[sharedNames],
> chain[sharedNames],  :
>  error in evaluating the argument 'x' in selecting a method for function
> 'unlist': Error in `[.default`(strandRevCodes, as.vector(flipped)) :
>  only 0's may be mixed with negative subscripts
>
>
>
> I guess that the error wasn't noticed before since the example is set as
> notrun. I guess that's simply because of the process of getting the chain
> file.
>
> Thank you for your help.
>
> Cheers,
> Leonardo
>
>
> Here is my session information:
>
> > sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2
> [2] GenomicFeatures_1.6.4
> [3] AnnotationDbi_1.16.8
> [4] Biobase_2.14.0
> [5] rtracklayer_1.14.4
> [6] RCurl_1.7-0
> [7] bitops_1.0-4.1
> [8] GenomicRanges_1.6.4
> [9] IRanges_1.12.4
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.10.0    Biostrings_2.22.0 BSgenome_1.22.0   DBI_0.2-5
> [5] RSQLite_0.10.0    tools_2.14.0      XML_3.4-3         zlibbioc_1.0.0
>
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>
>
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