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aertslab / AUCell

AUCell: score single cells with gene regulatory networks
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Avoid overwriting BiocGenerics::cbind #9

Closed LTLA closed 4 years ago

LTLA commented 4 years ago

It seems that AUCell is setting its own generic for cbind, which displaces BiocGenerics::cbind:

library(SummarizedExperiment)
example(SummarizedExperiment)
cbind(se, se) # okay, gives another SE

library(AUCell)
cbind(se, se) # wrong, gives a matrix of 2 SEs.

This does not play nice with analyses involving other Bioconductor packages, which is not good. Fortunately, it is easily resolved by implementing methods on BiocGenerics::cbind instead. In fact, you're importing it anyway, so it should just be as simple as deleting the setGeneric calls.

Session info ``` R Under development (unstable) (2020-02-05 r77773) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS Matrix products: default BLAS: /home/luna/Software/R/trunk/lib/libRblas.so LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] AUCell_1.9.0 SummarizedExperiment_1.17.2 [3] DelayedArray_0.13.4 BiocParallel_1.21.2 [5] matrixStats_0.55.0 Biobase_2.47.2 [7] GenomicRanges_1.39.2 GenomeInfoDb_1.23.13 [9] IRanges_2.21.3 S4Vectors_0.25.12 [11] BiocGenerics_0.33.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.3 later_1.0.0 compiler_4.0.0 [4] XVector_0.27.0 R.methodsS3_1.8.0 R.utils_2.9.2 [7] bitops_1.0-6 tools_4.0.0 zlibbioc_1.33.1 [10] digest_0.6.24 bit_1.1-15.2 annotate_1.65.1 [13] RSQLite_2.2.0 memoise_1.1.0 lattice_0.20-38 [16] rlang_0.4.4 Matrix_1.2-18 graph_1.65.1 [19] shiny_1.4.0 DBI_1.1.0 fastmap_1.0.1 [22] GenomeInfoDbData_1.2.2 vctrs_0.2.2 bit64_0.9-7 [25] grid_4.0.0 GSEABase_1.49.0 data.table_1.12.8 [28] R6_2.4.1 AnnotationDbi_1.49.1 XML_3.99-0.3 [31] magrittr_1.5 blob_1.2.1 promises_1.1.0 [34] htmltools_0.4.0 mime_0.9 xtable_1.8-4 [37] httpuv_1.5.2 RCurl_1.98-1.1 R.oo_1.23.0 ```
s-aibar commented 4 years ago

Thanks! It should be solved now...