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 * 0 packages out-of-date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 0 packages out-of-date; 1 packages too new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.b...@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-boun...@r-project.org on behalf of nlhuon...@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
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
--
-Lan
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