[Bioc-devel] SummarizedExperiment warning upon loading

[Lan Huong Nguyen]

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   * 0 packages out-of-date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 0 packages out-of-date; 1 packages too new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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>
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>     Bioc-devel using r-project.org mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

-- 
-Lan

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