Silvia,

I understand that you cannot send the whole dataset. Could you please just send me the chromosome,strand, start and end information for the row that caused the problem so that I can try to reproduce the error? Also, could you please update ChIPpeakAnno to 2.6  and see if that resolves the problem http://www.bioconductor.org/packages/2.11/bioc/html/ChIPpeakAnno.html? Thanks!

Best regards,

Julie


On 1/14/13 11:23 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com> wrote:

Hello,

thanks for the quick response. Unfortunately I cannot supply the data, but the session info is the following:

sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

attached base packages:
[1] grid      stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
 [1] coda_0.15-2                         rGADEM_2.4.0
 [3] seqLogo_1.22.0                      cureos_0.3
 [5] multicore_0.1-7                     BayesPeak_1.8.0
 [7] org.Mm.eg.db_2.7.1                  rtracklayer_1.16.3
 [9] ShortRead_1.14.4                    latticeExtra_0.6-24
[11] RColorBrewer_1.0-5                  Rsamtools_1.8.6
[13] lattice_0.20-10                     BSgenome.Mmusculus.UCSC.mm9_1.3.17
[15] BiocInstaller_1.4.9                 ChIPpeakAnno_2.4.0
[17] limma_3.12.3                        org.Hs.eg.db_2.7.1
[19] GO.db_2.7.1                         RSQLite_0.11.2
[21] DBI_0.2-5                           AnnotationDbi_1.18.4
[23] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0
[25] GenomicRanges_1.8.13                Biostrings_2.24.1
[27] IRanges_1.14.4                      multtest_2.12.0
[29] Biobase_2.16.0                      biomaRt_2.12.0
[31] BiocGenerics_0.2.0                  gplots_2.11.0
[33] MASS_7.3-22                         KernSmooth_2.23-8
[35] caTools_1.13                        bitops_1.0-4.1
[37] gdata_2.12.0                        gtools_2.7.0

loaded via a namespace (and not attached):
[1] hwriter_1.3      RCurl_1.95-1.1   splines_2.15.0   stats4_2.15.0
[5] survival_2.36-14 tools_2.15.0     XML_3.95-0.1     zlibbioc_1.2.0

I ithink it should be related to IRanges package...
My output.1 data object (used as input when the problem occurs) has the following start ranges and width
 range(output.1$ranges@start)
[1]   2999950 194976340
range(output.1$ranges@width)
[1]  101 3551

Many thanks!

2013/1/14 Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu>
Dear Silvia,

Could you please send me the test data and code that resulted in this error message? Please also send me your session information as well.  Thanks!

Best regards,

Julie



On 1/14/13 6:33 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com <http://silvia.heyde@gmail.com> > wrote:

Hello!

I have a problem with the function mentioned above (should be solve_user_SEW invoked by getAllPeakSequence) and I hope you can help me.
I get an error:
"in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  : solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (130043477) is > refwidth + 1"
I've already read in some mailing lists that this is known but I did not find any solution for that.

Many thanks in advance,
Silvia



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