Thanks for noticing that. I'll fix that in R soon. I'm going through and generalizing many of the stats default methods so that they work automatically with Rle.
For order,Rle(), I fixed the method argument default and added a fast path for the single arg case. I guess we'll keep it around. On Thu, May 11, 2017 at 6:47 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > 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 >>>> >>>> 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" <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]] >>>> > >>>> > _______________________________________________ >>>> > Bioc-devel@r-project.org mailing list >>>> > >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FhYaKPjNM3nCK5wrqNrek8IgmU7YlJH8B77AMM77j7U&s=N1wtJXFb6nsvQncKFe8tgzi_q8NunVLhu-gJoQA_Co8&e= >>>> >>>> > >>>> >>>> -- >>>> 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 >>>> >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=SfDjGrm-go9CSXhsmi7cU43TGLLM-77DG5Lpdg0dD8U&s=SAYmrM-Cxa3tQ7XDNei_qKHzwjdLRoa-aQCt9W03Fs8&e= >>>> >> > > -- > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel