List extraction via `[` is failing due to downstream `updateObject` call

[mjsteinbaugh]

Hi, I seem to have hit a bug in S4Vectors for objects that extend SimpleList. Attempting to subset the list via [ extraction is now returning an error in Bioconductor 3.10, due to a downstream issue with BiocGenerics::updateObject(x, check = FALSE) being called internally.

Here's an example:

## https://github.com/acidgenomics/pfgsea
data(gsea, package = "pfgsea")
class(gsea)
## [1] "FGSEAList"
## attr(,"package")
## [1] "pfgsea

Let's take a look at the S4 class structure, which extends SimpleList:

showClass("FGSEAList")

Class "FGSEAList" [package "pfgsea"]

Slots:
                                                                              
Name:           listData       elementType   elementMetadata          metadata
Class:              list         character DataTable_OR_NULL              list

Extends: 
Class "SimpleList", directly
Class "List", by class "SimpleList", distance 2
Class "Vector", by class "SimpleList", distance 3
Class "list_OR_List", by class "SimpleList", distance 3
Class "Annotated", by class "SimpleList", distance 4
Class "vector_OR_Vector", by class "SimpleList", distance 4

This example object only has 1 element, but the same error returns for similar objects with multiple elements defined in the list.

length(gsea)
## [1] 1

Extraction of a single element via [[ works as expected.

gsea[[1]]

However, an attempt to subset the list via [ currently errors out.

gsea[1]

Error in .local(object, ...) : unused argument (check = FALSE)
Calls: [ ... extractROWS -> extractROWS -> updateObject -> updateObject
Backtrace:
    █
 1. ├─gsea[1]
 2. └─gsea[1]
 3.   └─S4Vectors:::subset_along_ROWS(x, i, drop = drop)
 4.     ├─S4Vectors::extractROWS(x, i)
 5.     └─S4Vectors::extractROWS(x, i)
 6.       ├─BiocGenerics::updateObject(x, check = FALSE)
 7.       └─pfgsea::updateObject(x, check = FALSE)

I'm not seeing this error when I don't have an updateObject method defined for the object.

Here's my session info via utils::sessionInfo():

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pfgsea_0.1.15    basejump_0.11.21 bb8_0.2.2

loaded via a namespace (and not attached):
  [1] fgsea_1.12.0                  colorspace_1.4-1
  [3] grr_0.9.5                     ggridges_0.5.1
  [5] htmlTable_1.13.2              XVector_0.26.0
  [7] GenomicRanges_1.38.0          base64enc_0.1-3
  [9] rstudioapi_0.10               ggrepel_0.8.1
 [11] bit64_0.9-7                   interactiveDisplayBase_1.24.0
 [13] AnnotationDbi_1.48.0          splines_3.6.1
 [15] R.methodsS3_1.7.1             goalie_0.4.0
 [17] geneplotter_1.64.0            knitr_1.25
 [19] zeallot_0.1.0                 Formula_1.2-3
 [21] Rsamtools_2.2.0               annotate_1.64.0
 [23] freerange_0.2.8               cluster_2.1.0
 [25] dbplyr_1.4.2                  R.oo_1.23.0
 [27] pheatmap_1.0.12               shiny_1.4.0
 [29] BiocManager_1.30.9            compiler_3.6.1
 [31] httr_1.4.1                    backports_1.1.5
 [33] assertthat_0.2.1              Matrix_1.2-17
 [35] fastmap_1.0.1                 lazyeval_0.2.2
 [37] acidbase_0.1.1                cli_1.1.0
 [39] later_1.0.0                   acepack_1.4.1
 [41] htmltools_0.4.0               prettyunits_1.0.2
 [43] tools_3.6.1                   gtable_0.3.0
 [45] glue_1.3.1                    GenomeInfoDbData_1.2.2
 [47] transformer_0.2.10            dplyr_0.8.3
 [49] acidplots_0.2.16              rappdirs_0.3.1
 [51] fastmatch_1.1-0               Rcpp_1.0.2
 [53] Biobase_2.46.0                vctrs_0.2.0
 [55] Biostrings_2.54.0             rtracklayer_1.46.0
 [57] xfun_0.10                     stringr_1.4.0
 [59] brio_0.3.15                   syntactic_0.3.2
 [61] mime_0.7                      ensembldb_2.10.0
 [63] XML_3.98-1.20                 AnnotationHub_2.18.0
 [65] zlibbioc_1.32.0               scales_1.0.0
 [67] hms_0.5.2                     promises_1.1.0
 [69] ProtGenerics_1.18.0           parallel_3.6.1
 [71] SummarizedExperiment_1.16.0   AnnotationFilter_1.10.0
 [73] RColorBrewer_1.1-2            SingleCellExperiment_1.8.0
 [75] yaml_2.2.0                    curl_4.2
 [77] gridExtra_2.3                 memoise_1.1.0
 [79] UpSetR_1.4.0                  ggplot2_3.2.1
 [81] Matrix.utils_0.9.7            rpart_4.1-15
 [83] biomaRt_2.42.0                latticeExtra_0.6-28
 [85] stringi_1.4.3                 RSQLite_2.1.2
 [87] genefilter_1.68.0             BiocVersion_3.10.1
 [89] S4Vectors_0.24.0              checkmate_1.9.4
 [91] GenomicFeatures_1.38.0        BiocGenerics_0.32.0
 [93] BiocParallel_1.20.0           GenomeInfoDb_1.22.0
 [95] rlang_0.4.1                   pkgconfig_2.0.3
 [97] matrixStats_0.55.0            bitops_1.0-6
 [99] lattice_0.20-38               purrr_0.3.3
[101] htmlwidgets_1.5.1             GenomicAlignments_1.22.0
[103] cowplot_1.0.0                 bit_1.1-14
[105] tidyselect_0.2.5              plyr_1.8.4
[107] magrittr_1.5                  DESeq2_1.26.0
[109] R6_2.4.0                      IRanges_2.20.0
[111] Hmisc_4.2-0                   DelayedArray_0.12.0
[113] DBI_1.0.0                     pillar_1.4.2
[115] foreign_0.8-72                withr_2.1.2
[117] survival_3.1-6                RCurl_1.95-4.12
[119] nnet_7.3-12                   tibble_2.1.3
[121] crayon_1.3.4                  BiocFileCache_1.10.0
[123] progress_1.2.2                locfit_1.5-9.1
[125] grid_3.6.1                    data.table_1.12.6
[127] blob_1.2.0                    bioverbs_0.2.10
[129] digest_0.6.22                 xtable_1.8-4
[131] httpuv_1.5.2                  DESeqAnalysis_0.2.10
[133] R.utils_2.9.0                 openssl_1.4.1
[135] stats4_3.6.1                  munsell_0.5.0
[137] sessioninfo_1.1.1             askpass_1.1