Warning when loading package

[nicolerg]

Hello, I am getting the following warning when I load cmapR, either directly with library(cmapR) or by importing cmapR as a dependency for an R package:

Warning messages:
1: multiple methods tables found for ‘aperm’ 
2: replacing previous import ‘BiocGenerics::aperm’ by ‘DelayedArray::aperm’ when loading ‘SummarizedExperiment’ 

This is preventing me from having a passing R-CMD-check for an R package I am developing with cmapR as a dependency.

sessionInfo:

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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     

other attached packages:
[1] cmapR_1.8.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9                  lattice_0.20-45             matrixStats_0.63.0          IRanges_2.30.1              RProtoBufLib_2.8.0         
 [6] bitops_1.0-7                grid_4.2.2                  GenomeInfoDb_1.32.4         stats4_4.2.2                RcppParallel_5.1.6         
[11] zlibbioc_1.42.0             XVector_0.36.0              flowCore_2.8.0              S4Vectors_0.34.0            Matrix_1.5-3               
[16] tools_4.2.2                 Biobase_2.58.0              RCurl_1.98-1.9              DelayedArray_0.22.0         MatrixGenerics_1.8.1       
[21] compiler_4.2.2              BiocGenerics_0.44.0         cytolib_2.8.0               GenomicRanges_1.48.0        SummarizedExperiment_1.26.1
[26] GenomeInfoDbData_1.2.8     

[tnat1031]

Hi @nicolerg,

I think this issue is a namespace collision for the aperm method. It seems that as of version 0.22.0 the DelayedArray package was exporting a method named aperm, which is colliding with the aperm method from the BiocGenerics package, both of which are being imported by SummarizedExperiment. This seems to have been fixed in DelayedArray version 0.24.0. Could you try updating the Imports section of your DESCRIPTION file to require DelayedArray>= 0.24.0 to see if that fixes it?

Thanks a lot,
Ted

[nicolerg]

Hi @tnat1031, thank you for the quick reply! Upgrading to DelayedArray 0.24.0 resolved the warning. Thank you for your help.

[tnat1031]

Great, glad that worked!

…

On Sat, Jan 14, 2023, 1:18 PM Nicole Gay, PhD ***@***.***> wrote: Hi @tnat1031 <https://github.com/tnat1031>, thank you for the quick reply! Upgrading to DelayedArray 0.24.0 resolved the warning. Thank you for your help. — Reply to this email directly, view it on GitHub <#70 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F3ZO3UJ6OMZ7GHPRVMDWSLUYTANCNFSM6AAAAAAT3CAG2E> . You are receiving this because you were mentioned.Message ID: ***@***.***>