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...@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
