SingleR Error in getMethod(generic, "ANY")
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inzirio ▴ 10
@inzirio-13571
Last seen 5 months ago

I'm using the latest version of R and Bioconductor 3.12, but today, after a few updates, I got this error:

Error in getMethod(generic, "ANY") : 
  no method found for function 'rowMedians' and signature ANY

I got the same error with the SingleR example:

ref <- .mockRefData()
test <- .mockTestData(ref)

ref <- scuttle::logNormCounts(ref)
test <- scuttle::logNormCounts(test)

# Running the classification with different options:
pred <- SingleR(test, ref, labels=ref$label)

This is my sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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  methods   base     

other attached packages:
 [1] SingleR_1.3.11               MultiAssayExperiment_1.15.10 SpatialExperiment_0.99.3    
 [4] SingleCellExperiment_1.11.8  SummarizedExperiment_1.19.9  Biobase_2.49.1              
 [7] GenomicRanges_1.41.6         GenomeInfoDb_1.25.11         IRanges_2.23.10             
[10] MatrixGenerics_1.1.7         matrixStats_0.57.0           S4Vectors_0.27.14           
[13] BiocGenerics_0.35.4          Matrix_1.2-18               

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                    rsvd_1.0.3                    lattice_0.20-41              
 [4] assertthat_0.2.1              digest_0.6.26                 mime_0.9                     
 [7] BiocFileCache_1.13.1          R6_2.4.1                      RSQLite_2.2.1                
[10] httr_1.4.2                    pillar_1.4.6                  sparseMatrixStats_1.1.11     
[13] zlibbioc_1.35.0               rlang_0.4.8                   curl_4.3                     
[16] SingleCellMultiModal_1.1.16   rstudioapi_0.11               irlba_2.3.3                  
[19] blob_1.2.1                    BiocNeighbors_1.7.0           BiocParallel_1.23.3          
[22] AnnotationHub_2.21.5          RCurl_1.98-1.2                bit_4.0.4                    
[25] beachmat_2.5.8                shiny_1.5.0                   DelayedArray_0.15.16         
[28] httpuv_1.5.4                  compiler_4.0.3                BiocSingular_1.5.2           
[31] pkgconfig_2.0.3               htmltools_0.5.0               tidyselect_1.1.0             
[34] tibble_3.0.4                  GenomeInfoDbData_1.2.4        interactiveDisplayBase_1.27.5
[37] later_1.1.0.1                 crayon_1.3.4                  dplyr_1.0.2                  
[40] dbplyr_1.4.4                  bitops_1.0-6                  rappdirs_0.3.1               
[43] grid_4.0.3                    xtable_1.8-4                  lifecycle_0.2.0              
[46] DBI_1.1.0                     magrittr_1.5                  scuttle_0.99.20              
[49] XVector_0.29.3                promises_1.1.1                DelayedMatrixStats_1.11.4    
[52] ellipsis_0.3.1                generics_0.0.2                vctrs_0.3.4                  
[55] tools_4.0.3                   bit64_4.0.5                   glue_1.4.2                   
[58] purrr_0.3.4                   BiocVersion_3.12.0            fastmap_1.0.1                
[61] yaml_2.2.1                    AnnotationDbi_1.51.3          ExperimentHub_1.15.3         
[64] BiocManager_1.30.10           memoise_1.1.0

Any help is appreciated!

Thanks, Dario

singleR rowMedians getMethod • 460 views
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I am having the same Issue since an update yesterday

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Aaron Lun ★ 26k
@alun
Last seen 2 hours ago
The city by the bay

Sit tight and wait for DelayedMatrixStats 1.11.5 to hit the shelves.

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Does anybody know which specific package update is responsible for the error and how I can install a previous version of it, so SingleR works again?

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0
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Yes, I just said it above.

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0
Entering edit mode

Updating DelayedMatrixStats to version 1.11.5 didn't work for me. Instead I downgraded to SingleR 1.2.4 and it worked again!

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