On 05/11/2017 06:44 PM, Hervé Pagès wrote:
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:
Forgot to copy/paste this:
library(S4Vectors)
x <- Rle(sample(25L, 500000L, replace=TRUE) - 8L,
sample(13L, 500000L, replace=TRUE))
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
and to provide my sessionInfo():
> sessionInfo()
R version 3.4.0 Patched (2017-04-26 r72630)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.4.r72630/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.4.r72630/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] S4Vectors_0.15.2 BiocGenerics_0.23.0
loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0
H.
H.
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
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>
>
>
> [[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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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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
Fax: (206) 667-1319
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