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* 0 packages out-of-date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0 packages out-of-date; 1 packages too new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