Latest SingleCellExperiment breaks buildCellTypeIndex

[letaylor]

An update to SingleCellExperiment causes buildCellTypeIndex to break producing the following error:
Error: $ operator not defined for this S4 class

I think it is this commit that changed ShallowSimpleListAssays to SimpleAssays:
Bioconductor/SummarizedExperiment@e8a159a

  library("scfind")
  library("SingleCellExperiment")
  data(tmfacs)
   sce.bladder <- readRDS(url(tmfacs[1]))
    sce.bladder_updated <- SingleCellExperiment(
        assays = list(counts = counts(sce.bladder)),
        colData = colData(sce.bladder)
    )
    scfind.index <- scfind::buildCellTypeIndex(
        sce = sce.bladder_updated,
        cell.type.label = "cell_type1",
        dataset.name = "Bladder",
        assay.name = "counts"
    )

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/ubuntu/miniconda3/envs/sc_analysis_nb/lib/libopenblasp-r0.3.7.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] SingleCellExperiment_1.8.0  SummarizedExperiment_1.16.1
 [3] DelayedArray_0.12.2         BiocParallel_1.20.1
 [5] matrixStats_0.56.0          Biobase_2.46.0
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0
 [9] IRanges_2.20.2              S4Vectors_0.24.3
[11] BiocGenerics_0.32.0         scfind_3.5.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4             later_1.0.0            compiler_3.6.2
 [4] pillar_1.4.3           XVector_0.26.0         bitops_1.0-6
 [7] tools_3.6.2            zlibbioc_1.32.0        digest_0.6.25
[10] lifecycle_0.2.0        tibble_2.1.3           gtable_0.3.0
[13] lattice_0.20-40        pkgconfig_2.0.3        rlang_0.4.5
[16] Matrix_1.2-18          shiny_1.4.0.2          fastmap_1.0.1
[19] GenomeInfoDbData_1.2.2 dplyr_0.8.5            htmlwidgets_1.5.1
[22] tidyselect_1.0.0       grid_3.6.2             DT_0.12
[25] glue_1.3.2             data.table_1.12.8      R6_2.4.1
[28] hash_2.2.6.1           purrr_0.3.3            ggplot2_3.3.0
[31] magrittr_1.5           codetools_0.2-16       promises_1.1.0
[34] scales_1.1.0           htmltools_0.4.0        assertthat_0.2.1
[37] xtable_1.8-4           mime_0.9               colorspace_1.4-1
[40] httpuv_1.5.2           RCurl_1.98-1.1         munsell_0.5.0
[43] crayon_1.3.4

[thjimmylee]

Hi, @letaylor

Thanks for the pull request. I am now trying a different way to ensure a better compatibility for both versions of SingleCellExperiment object. Would you mind helping us to test this branch instead?

devtools::install_github("hemberg-lab/scfind", ref = "RELEASE_3_6”)

In the near future, we will also allow index building from just the raw matrix and metadata.

[thjimmylee]

Thanks for the spot. Problem resolved by enabling version compatibility. Please try the new version.