[Bioc-devel] SummarizedExperiment warning upon loading

[Martin Morgan]

Please try re-installing BiocGenerics. It might also be necessary to reinstall other packages in 'XVector', 'S4Vectors', 'IRanges', "GenomicRanges'

I believe the problem is that the 'lengths' generic was implemented in base R and then removed from BiocGenerics, but that one or more of your installed packages was installed prior to the updated version of base R and has cached the two methods tables -- for the new base R and the old BiocGenerics. You could be more surgical about this by setting options(warn = 2) before trying to load SummarizedExperiment. This would trigger an error, and comparing the packages that successfully loaded (via sessionInfo()) would eliminate them from need to update.

Also the issue with BiocParallel version is likely because there are two (or more versions) of BiocParallel installed in your .libPaths(); you are updating the 'first' version on .libPaths(), but BiocManager::valid() is finding both and complaining about the un-updated version appearing in a later .libPaths().

Martin

On 12/3/18, 1:53 PM, "Lan Huong Nguyen" <nlhuong90 using gmail.com> wrote:

    Thank you for the advice! I checked validity of the packages and reinstalled "too new" once appearing in the warning.
    However, I could not install a correct BiocParallel version using 
    
    
    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install("BiocParallel", version = "3.9")
    I obtain BiocParallel 1.17.3 not 1.17.1, and calling BiocManager::valid() I get the following returned:
    
    
    
    > BiocManager::valid()
    * sessionInfo()
    R Under development (unstable) (2018-11-30 r75722)
    Platform: x86_64-apple-darwin15.6.0 (64-bit)
    Running under: macOS Mojave 10.14.1
    Matrix products: default
    BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats     graphics  grDevices utils     datasets  methods   base     
    loaded via a namespace (and not attached):
    [1] BiocManager_1.30.4 compiler_3.6.0     tools_3.6.0        yaml_2.2.0        
    Bioconductor version '3.9'
      * 0 packages out-of-date
      * 1 packages too new
    create a valid installation with
      BiocManager::install("BiocParallel", update = TRUE, ask = FALSE)
    more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
    Warning message:
    0 packages out-of-date; 1 packages too new 
    
    
    
    Starting a fresh session and loading SummarizedExperiment I still obtain the warning:
    
    
    
    Warning message:
    multiple methods tables found for ‘lengths’
    
    
    
    and the sessionInfo() gives:
    
    
    
    R Under development (unstable) (2018-11-30 r75722)
    Platform: x86_64-apple-darwin15.6.0 (64-bit)
    Running under: macOS Mojave 10.14.1
    Matrix products: default
    BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel  stats4    stats     graphics  grDevices utils     datasets 
    [8] methods   base     
    other attached packages:
     [1] SummarizedExperiment_1.13.0 DelayedArray_0.9.0         
     [3] BiocParallel_1.17.3         matrixStats_0.54.0         
     [5] Biobase_2.43.0              GenomicRanges_1.35.1       
     [7] GenomeInfoDb_1.19.1         IRanges_2.17.1             
     [9] S4Vectors_0.21.6            BiocGenerics_0.29.1        
    loaded via a namespace (and not attached):
     [1] lattice_0.20-38        bitops_1.0-6           grid_3.6.0            
     [4] zlibbioc_1.29.0        XVector_0.23.0         Matrix_1.2-15         
     [7] tools_3.6.0            RCurl_1.95-4.11        yaml_2.2.0            
    [10] compiler_3.6.0         GenomeInfoDbData_1.2.0
    
    
     
    
    Let me know if you see a potential fix.
    
    
    Best,
    Lan
    
    
    
    
    
    On Sun, Dec 2, 2018 at 9:38 AM Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
    
    
    A good place to start is to verify that your packages are all from the same release
    
    BiocManager::valid()
    
    and then if that is not revealing make sure to start a new R session, attach SummarizedExperiment, and report the output of sessionInfo().
    
    Martin
    
    On 12/1/18, 8:16 PM, "Bioc-devel on behalf of Lan Huong Nguyen" <bioc-devel-bounces using r-project.org on behalf of
    nlhuong90 using gmail.com> wrote:
    
        Hi everyone,
    
        I am working with R 3.6 on macOS mojave, and I installed the
        SummarizedExperiment from BiocManager 3.9. Whenever the package is loaded I
        get the following warning:
    
        Warning: multiple methods tables found for ‘lengths'
    
        Did anyone encounter this problem? Any suggestions for fixes?
    
        Best,
        Lan
    
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    -- 
    -Lan