[Bioc-devel] Question about BiocGeneric::order
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.Ou at umassmed.edu> wrote:
Thank you Herv?,
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, "Herv? Pag?s" <hpages at 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.
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--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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