[Bioc-devel] Question about BiocGeneric::order

[Hervé Pagès]

Hi Michael,

On 05/11/2017 03:27 PM, Michael Lawrence wrote:
> 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.

Note that base::order() is much slower than the method for Rle objects:

 > system.time(oo1 <- order(x))
    user  system elapsed
   0.018   0.000   0.018

 > system.time(oo2 <- base::order(x))
    user  system elapsed
   1.089   0.000   1.103

 > identical(oo1, oo2)
[1] TRUE

Looks like by default, base::order() does not pick up the fastest
method (radix):

 > system.time(oo2 <- base::order(x, method="radix"))
    user  system elapsed
   0.020   0.000   0.019

H.

>
> Michael
>
> On Thu, May 11, 2017 at 1:29 PM, Ou, Jianhong <Jianhong.Ou at 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
>>
>> 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.
>>
>>
>>
>>
>>
>> On 5/11/17, 4:25 PM, "Hervé Pagès" <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.
>>     >
>>     >
>>     >
>>     >   [[alternative HTML version deleted]]
>>     >
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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: hpages at fredhutch.org
>>     Phone:  (206) 667-5791
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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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319