[Bioc-devel] Question about BiocGeneric::order

[Ou, Jianhong]

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]]
    >
    > _______________________________________________
    > Bioc-devel at 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: hpages at fredhutch.org
    Phone:  (206) 667-5791
    Fax:    (206) 667-1319