There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods
package (recently fixed in devel), the bug is masked. So, we should
fix S4Vectors. The problem is that order,Rle has a default for the
'method' argument that differs from that of the generic. Since R 3.3,
base::order() is smart enough to basically do the same thing as
order,Rle(). I'll go ahead and remove the method.
Michael
On Thu, May 11, 2017 at 1:29 PM, Ou, Jianhong <jianhong...@umassmed.edu> wrote:
> Thank you Hervé,
>
> I got that. Good to know that BioC 3.6 require R 3.4.0.
>
> Yours Sincerely,
>
> Jianhong Ou
>
> TEL: 508-856-5379
> LRB 608
> Bioinformatician of Bioinformatics core at
> Department of Molecular, Cell and Cancer Biology
> UMASS Medical School
> 364 Plantation Street Worcester,
> MA 01605
>
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>
>
> On 5/11/17, 4:25 PM, "Hervé Pagès" <hpa...@fredhutch.org> wrote:
>
> Hi Jianhong,
>
> I can't reproduce this but I'm using R 3.4.0.
> You seem to be using Bioc devel (aka BioC 3.6) with R devel.
> This is not supported. Both, BioC 3.5 (current release) and
> BioC 3.6 require R 3.4.0.
>
> Cheers,
> H.
>
>
> On 05/11/2017 01:11 PM, Ou, Jianhong wrote:
> > I got error when I try order for Rle object by following codes:
> >
> > library("BiocGenerics")
> > library(XVector)
> > order(Rle(1))
> > ## Error in match.arg(method) : 'arg' must be of length 1
> >
> >> sessionInfo()
> > R Under development (unstable) (2017-05-10 r72667)
> > Platform: x86_64-apple-darwin16.5.0 (64-bit)
> > Running under: macOS Sierra 10.12.4
> >
> > Matrix products: default
> > BLAS:
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib
> > LAPACK:
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> >
> > 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] stats4 parallel stats graphics grDevices utils datasets
> > [8] methods base
> >
> > other attached packages:
> > [1] XVector_0.17.0 IRanges_2.11.2 S4Vectors_0.15.1
> > [4] BiocGenerics_0.23.0
> >
> > loaded via a namespace (and not attached):
> > [1] zlibbioc_1.23.0 compiler_3.5.0
> >
> > Is this a bug? Or I should always add method argument?
> >
> > Yours Sincerely,
> >
> > Jianhong Ou
> >
> > TEL: 508-856-5379
> > LRB 608
> > Bioinformatician of Bioinformatics core at
> > Department of Molecular, Cell and Cancer Biology
> > UMASS Medical School
> > 364 Plantation Street Worcester,
> > MA 01605
> >
> > Confidentiality Notice:
> > This e-mail message, including any attachments, is for the sole use of
> the intended recipient(s) and may contain confidential, proprietary and
> privileged information. Any unauthorized review, use, disclosure or
> distribution is prohibited. If you are not the intended recipient, please
> contact the sender immediately and destroy or permanently delete all copies
> of the original message.
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> >
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> >
>
> --
> 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
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
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>
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