Thank you very much Tengfei!


On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote:

> Hi
>
> I just fixed this bug in 1.10.1 in release branch, please update one or
> two days later.
>
> Thanks
>
> Tengfei
>
>
> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote:
>
>> Hi Leonardo,
>>
>> Thanks for reporting the issue, this is probably not R's problem, should
>> be a bug in ggbio's new class, I will look into this.
>>
>> Tengfei
>>
>>
>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres <
>> lcollado@jhsph.edu> wrote:
>>
>>> Dear BioC list and Tengfei Yin,
>>>
>>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2
>>> that I think is related to changes in R. The error can also be seen in
>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf (search
>>> 'unnamed' on the pdf).
>>>
>>> Below is the error from running the example code for plotIdeogram.
>>>
>>> library(ggbio)
>>> library(biovizBase)
>>> data(hg19IdeogramCyto, package = "biovizBase")
>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE
>>> plotIdeogram(hg19IdeogramCyto, "chr1")
>>>
>>> ## Error in initialize(value, ...) :
>>>   unnamed argument must extend either the S3 class or the class of the
>>> data part; not true of class “GGbio”
>>>
>>> traceback()
>>>
>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class or
>>> the class of the data part; not true of class %s",
>>> ##       dQuote(Classi)), domain = NA)
>>> ## 5: initialize(value, ...)
>>> ## 4: initialize(value, ...)
>>> ## 3: new("Ideogram", x)
>>> ## 2: Ideogram(p)
>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1")
>>>
>>> sessionInfo()
>>>
>>> ## R version 3.0.2 (2013-09-25)
>>> ## Platform: x86_64-apple-darwin10.8.0 (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] biovizBase_1.10.0 ggbio_1.10.0      ggplot2_0.9.3.1
>>>
>>> ## loaded via a namespace (and not attached):
>>> ##  [1] AnnotationDbi_1.24.0    Biobase_2.22.0
>>>  BiocGenerics_0.8.0      biomaRt_2.18.0          Biostrings_2.30.0
>>> ##  [6] bitops_1.0-6            BSgenome_1.30.0         cluster_1.14.4
>>>        colorspace_1.2-4        DBI_0.2-7
>>> ## [11] dichromat_2.0-0         digest_0.6.3
>>>  GenomicFeatures_1.14.0  GenomicRanges_1.14.3    grid_3.0.2
>>> ## [16] gridExtra_0.9.1         gtable_0.1.2            Hmisc_3.12-2
>>>        IRanges_1.20.4          labeling_0.2
>>> ## [21] lattice_0.20-24         MASS_7.3-29             munsell_0.4.2
>>>         parallel_3.0.2          plyr_1.8
>>> ## [26] proto_0.3-10            RColorBrewer_1.0-5      RCurl_1.95-4.1
>>>        reshape2_1.2.2          rpart_4.1-3
>>> ## [31] Rsamtools_1.14.1        RSQLite_0.11.4
>>>  rtracklayer_1.22.0      scales_0.2.3            stats4_3.0.2
>>> ## [36] stringr_0.6.2           tools_3.0.2
>>> VariantAnnotation_1.8.2 XML_3.95-0.2            XVector_0.2.0
>>> ## [41] zlibbioc_1.8.0
>>>
>>>
>>> Thank you,
>>> Leonardo
>>>
>>> Leonardo Collado Torres, PhD student
>>> Department of Biostatistics
>>> Johns Hopkins University
>>> Bloomberg School of Public Health
>>> Website: http://www.biostat.jhsph.edu/~lcollado/
>>> Blog: http://lcolladotor.github.io/
>>>
>>
>>
>>
>> --
>> Tengfei Yin, PhD
>> Seven Bridges Genomics
>> sbgenomics.com
>> 625 Mt. Auburn St. Suite #208
>> Cambridge, MA 02138
>> (617) 866-0446
>>
>
>
>
> --
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866-0446
>

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