cmap/cmapR

Warning when loading package

Closed this issue · 3 comments

nicolerg commented

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 commented

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 commented

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

tnat1031 commented